African Journal of Biochemistry Research Vol. 1 (2), pp. 019-023, July 2007 Available online at http://www.academicjournals.

org/AJBR 2007 Academic Journals

Full Length Research Paper

Numerical simulation of the internal vibrations of COOH group in amino-salicylic acids

Y. P. Singh1*, Ratnesh Das2 and R. A. Singh3
1

Department of Physics, Government Womens Polytechnic College, Sagar (MP), 470001, India. 2 Department of Chemistry, Dr. H. S. Gour University, Sagar (MP), 470001, India. 3 Department of Physics, Dr. H. S. Gour University, Sagar (MP), 470003 India.
Accepted 28 May, 2007

Our present work reports the IR spectra of amino substituted salicylic acids recorded by FTIR spectrometer and also simulated theoretically. The simulation was performed using GF matrix and AM1, PM3, DFT method. In this work, the following steps were taken: optimizing the geometry, computing the IR spectra and comparing it with experimental spectra. Assuming Cs point symmetry, vibrational assignments for the observed frequencies have been proposed. The spectra exhibit distinct features originating from low frequency vibrational modes caused by intra-molecular motion. Key words: o-amino salicylic acid, m-amino salicylic acid, p-amino salicylic acid, FTIR spectra, vibrational spectra, AM1, PM3, DFT, G-F Matrix. INTRODUCTION Salicylic acid contains both a hydroxyl and a carboxyl group, which react with either an acid or an alcohol. Salicylic acid has strong antiseptic and germicidal properties because it is a carboxylated phenol. The presence of the carboxyl group appears to enhance the antiseptic property. Many hair tonics and remedies for athletes foot, corns and warts employ the keratolytic action of salicylic . acid Volvo et al. (1983) calculated normal coordinates for salicylic acid molecule and proposed the assignment of the observed Raman and IR spectra. They found that C=O stretching modes are accounted for by specific interactions due to the symmetry characteristics and possible conformational changes in the solution. With the availability of powerful computers and the advent of efficient density functional theory (DFT) methods implemented in standard codes, structure and dynamics of systems containing a few tens o f atoms (even more) are now within reach. Vibrational spectra of small molecules of biological or pharmaceutical relevance are routinely treated combining DFT electronic structure calculations with a harmonic analysis (Bakker et al., 2004). Due to deficiencies of the quantum chemical calculations and / or due to the neglect of an harmonic effect, these frequencies are typically a few percent higher than the observed ones. Marck et al. (2002) studied theoretical simulation of the s stretching band for salicylic acid taking into account adiabatic couplings between the high-frequency O-H stretching and the low-frequency intermolecular O.......O stretching modes. Jadrijevic et al (2004) analyzed the structures and the spectral properties of salicylic acid and benzoic acids by means of FT-IR (Figures 1-3 and NMR spectro-scopy. We compared experimental results with calculated frequentcies of amino-salicylic acids using force matrix method and AM1, PM3 and DFT method. These methods were able to account breadth of spectrum as well as description of vibrational modes to encourage the application of a similar procedure to a larger and more complex group.
EXPERIMENTAL

*Corresponding author. E-mail: Y_P_S_2k@yahoo.com.

Amino salicylic acids were purchased from Sigma Chemical Company (USA). I.R. Spectra has been recorded in the liquid phase in

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Figure 1. FT-IR Spectra of 3-amino salicylic acid.

Figure 2. FT-IR Spectra of 4-amino salicylic acid.

Figure 3. FT-IR Spectra of 5-amino salicylic acid.

Singh et al.
G tt=
Calculated Wavenumbers (cm-1) 4000 3500 3000 2500 2000 1500 1000 500 0 0 1000 2000 3000 4000 Experimental Wavenumbers (cm-1) AM1 Method PM3 Method
3N

021

=1

St . St

Where dot represents the scalar product of two vectors and = 1/m , the reciprocal of the mass of atom . The AM1 and PM3 semi empirical approaches were performed as implemented in MOPAC program (1997) and the precise keywords were used. DFT calculations were performed using HYPER CHEM program (2002) at the B3LYP (1993) levels of theory with 631G* basis set (1989). The vibrational IR spectra were calculated at the B3LYP/ 6-31G* levels of theory. We have transformed the harmonic force fields, determined initially in the cartesian coordinates, were transformed to the force fields in the internal local coordinates. The force fields obtained were used to calculate the potential energy distribution (PED, 2001). Contributions greater than 10% are given.

Figure 4. Correlation diagram for experimental Vs calculated frequencies (AM1 and PM3 method) for 3-aminosalicylic acid.

RESULTS AND DISCUSSIONS We had employed a very large basis set for the computational of the frequencies. First infrared frequencies were calculated for the amino benzoic acids (Cs Symmetry) at the DFT (B3LYP), AM1, PM3 and G F Matrix level of theory. We can get information from computational vibrational spectra only when we compare it with experimental spectrum. Our results are given in Table 1. Due to an harmonicity, the harmonic vibrational frequencies were found to be lowered by1 to 3% in almost all cases except AM1 method. The number of internal vibrations for a group is given by 3m-3, where m is the number of atoms in the group. Thus COOH has 9 modes of vibrations. These modes are as follow; O-H Stretching, C-O Stretching, C=O Stretching, in-plane-rocking, in-plane bending of C-O, in-planebending of C=O, in-plane-bending of OH, out-of-plane wagging, and out-of-plane torsion. Antony et al. (2005) studied vibrational spectra of benzoic acid and got C=O -1 -1 Stretching at 1745 cm , C-O stretching at 1050 cm , C-O -1 in-plane bending at 594 cm , C=O in-plane bend-ing at -1 -1 1804 cm , OH stretch at 3785 cm , rocking mode at 554 -1 -1 cm , torsion mode at 594 cm and wagging mode at 441 -1 cm . Florio et al. (2003) observed C=O Stretching at -1 -1 1752 cm , C-O stretching at 1347 cm , C-O in-plane -1 -1 bending at 628 cm , OH stretch at 3785 cm , rocking -1 -1 mode at 628 cm , and wagging mode at 160 cm . In present study we get frequencies as shown in Table 1. Conclusions Theoretical semi-empirical quantum mechanical AM1, PM3, DFT and GF matrix calculations of the geometry and vibrational frequencies of the o-,m-,p- amino salicylic acids are presented in this paper and compared with infrared spectra. The calculated geometries and frequencies agree well (for DFT and G.F. Matrix) with the experimental ones, but there are some differences between frequencies mainly due to intermolecular interactions, an harmonicity and computational basis set. The results indicate that, the exchange functional proposed by Becke and the correlation functional of Lee, Yang and Parr with 631G* basis set is the optimal model for studying o-,m-,pamino benzoic acids. Figures 4 to 6 shows agreement

C a lc u la t e d W a v e n u m b e rs (c m -1 )

4000

3000

2000

1000 0 0 1000 2000 3000 4000 Experimental Wavenumbers ( cm-1)

Figure 5. Correlation diagram for experimental Vs calculated frequencies (G-F matrix method) for 3amino salicylic acid. the range 400 4000 cm-1 on Perkin-Elmer spectrometer Model 397. Preparation of KBr discs A small amount of finally grounded solid sample was intimately mixed with about 100 times or more than its weight of potassium bromide powder. The finely grounded mixture was than pressed under very high pressure in a press (about 10/cm2) to form a small pallet (about 1 - 2 mm thick and 1 cm in diameter). The accuracy of the measurements was estimated to be within 3 cm-1 and the resolution was better than 2 cm-1 through the entire range for both the spectra. Computational and theoretical details In noncomplex molecules, the G F Matrix is given by:G tt= 3Ni=1 (B ti B ti) 1/ mi where t, t = 1,2,3,, 3N-6 In which mi is the mass of the atom to which the subscript I refers and Bti , Bti are constants determined by geometry of molecule. Internal coordinate St are related with Cartesian displacement coordinate i as: St =
3N i=1 Bti i

where t = 1,2,3.., 3N-6 is obtained as:

On solving G.F. matrix for any atom

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Table 1. Internal vibrations of COOH group.

Mode of vibration O-H Stretching a

3-amino salicylic -1 acid (cm ) 3338(E) 3438.9(GF) 3417.9(AM1) 3432.8(PM3) 3347.8(DFT) 1856(E) 1846.3(GF) 1959.2(AM1) 1938.4(PM3) 1863.7(DFT) 1538(E) 1581.4(GF) 1590.9(AM1) 1603.7(PM3) 1542.7(DFT) 401(E) 408.3(GF) 414.5(AM1) 421.6(PM3) 409.1(DFT) 310(E) 311.8(GF) 318.2(AM1) 322.5(PM3) 312.4(DFT) 1461(E) 1460.6(GF) 1467.6(AM1) 1471.6(PM3) 1458.1(DFT) 633(E) 612.4(GF) 614.5(AM1) 623.6(PM3) 629.6(DFT) 510(E) 521.5(GF) 556.0(AM1) 549.1(PM3) 514.8(DFT) 761(E) 771.4(GF) 769.4(AM1) 751.7(PM3) 758.3(DFT)

4-amino salicylic -1 acid (cm ) 3397(E) 3416.5(GF) 3423.3(AM1) 3432.6(PM3) 3390.7(DFT) 1845(E) 1863.2(GF) 2075.5(AM1) 1973.5(PM3) 1852.6(DFT) 1592(E) 1581.1(GF) 1583.6(AM1) 1611.8(PM3) 1581.9(DFT) 450(E) 431.3(GF) 437.2(AM1) 431.6(PM3) 412.8(DFT) 374(E) 371.6(GF) 357.5(AM1) 328.5(PM3) 367.3(DFT) 1450(E) 1445.3(GF) 1451.8(AM1) 1470.1(PM3) 1452.7(DFT) 641(E) 639.2(GF) 632.9(AM1) 627.5(PM3) 638.1(DFT) 525(E) 531.5(GF) 535.4(AM1) 538.5(PM3) 518.4(DFT) 775(E) 768.2(GF) 769.9(AM1) 753.79PM3) 765.1(DFT)

5-amino salicylic -1 acid (cm ) 3409(E) 3400.3(GF) 3418.7(AM1) 3434.7(PM3) 3385.1(DFT) 1823(E) 1799.9(GF) 1801.2(AM1) 1874.8(PM3) 1849.2(DFT) 1584(E) 1570.2(GF) 1580.2(AM1) 1601.6(PM3) 1574.8(DFT) 465(E) 448.8(GF) 418.2(AM1) 438.1(PM3) 418.7(DFT) 327(E) 313.2(GF) 311.8(AM1) 325.6(PM3) 335.1(DFT) 1454(E) 1445.6(GF) 1451.7(AM1) 1462.7(PM3) 1459.1(DFT) 686(E) 665.3(GF) 656.3(AM1) 641.8(PM3) 672.3(DFT) 568(E) 548.8(GF) 532.8(AM1) 541.2(PM3) 553(DFT) 774(E) 770.1(GF) 776.5(AM1) 761.9(PM3) 779.2(DFT)

C-O Stretching

C=O Stretching

Bending C-O

Bending C=O

Bending OH

Rocking a

Wagging

Torsion

E:- Experimental frequencies; GF:- Theoretical frequencies calculated by GF Matrix method; AM1:Theoretical frequencies calculated by quantum mechanical AM1 MOPAC method; PM3:- Theoretical frequencies calculated by quantum mechanical PM3 MOPAC method; DFT:- Theoretical calculations were performed using HYPER CHEM program at the B3LYP levels of theory with 6-31G* basis set

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Figure 6. Correlation diagram for experimental Vs calculated frequencies (DFT method) for 3-amino salicylic acid.

Florio EL, Sibert EL, Zwier TS. (2001), Fluorescence-dip IR spectra of jet-cooled benzoic acid dimer in its ground and first excited singlet states. Faraday Discuss. 118: 315. Florio M, Zwier TS, Sibert EL (2003). Theoretical modeling of the OH stretch infrared spectrum of carboxylic acid dimers. J. Chem. Phy. 118: 4. Here WJ, Random, L, Schlyer PVR, Pople JA (1989). Ab initio Molecular- Orbital Theory, Wiley, New York. pp 112-121 Hyperchem Package 7 for molecular modeling, (2002) Hypercube Inc. http:// www.wavefun.com Jadrijevic M, Takac M, Topic D, (2004). FT-IR and NMR spectroscopic studies of salicylic acid derivatives. Acta Pharm. 54: 177-197 Marek B, Wojcik MJ, Zieba A (2002). Theoretical model fora tetrad of hydrogen bonds and its applications of infrared spectra of salicylic acid. Chem. Phys. 124: 084306 Volvo V, Colombo L, Furic K (1983). Vibrational spectrum and normal coordinate calculations of the salicylic acid molecule. J. Raman Spect. 14(5): 347-352. Williams and Wilkins (2002). Foyes Principle of Medicinal Chemistry, 5th, Edition, New York. pp 118-129 Win MOPAC- Molecular Orbital Program, (1997) Fujitsu Limited http:// www.software.fujitsu.com/jp/winmopac

between the experimental and calculated wave numbers. The graph is linear which shows that theoretical and experimental results are in good agreement. Similar graphs were obtained for m- and p- amino benzoic acids. ACKNOWLEDGEMENTS The authors are grateful to Director, Directorate of Technical Education-Madhya Pradesh, Bhopal and Head, Department of Physics, Dr. H.S.Gour University, Sagar (MP), India and Central Drug Research Institute, Lucknow India for IR spectra, Hypercube Inc for provid-ing, Hyperchem Package 7 for molecular modeling.
REFERENCES Antony J, Helden GV, Meijer G, Achmidt B (2005). An harmonic midinfrared vibrational spectra of benzoic acid monomer and dimer. J. Chem. Phys. 123: 014305. Bakker JM, Meyer G, Kabelac M, de Vries MS, (2004), The mid-IR absorption spectrum of gas-phase clusters of the nucleobases guanine and cytosine. Phys. Chem. Chem. Phys. 6: 2810. Becke AD (1993), Density-functional thermochemistry. III. The role of exact exchange, J. Chem. Phys. 98: 5648.

Calculated W avnum bers (cm -1)